Ambient occlusion – A powerful algorithm to segment shell and skeletal intrapores in computed tomography data

J. Titschack, D. Baum, K. Matsuyama, K. Boos, C. Farber, W.-A. Kahl, K. Ehrig, D. Meinel, C. Soriano, S.R. Stock - MARUM, Center of Marine Environmental Sciences, University of Bremen, Bremen, Germany; SaM, Senckenberg am Meer, Abteilung Meeresforschung, Wilhelmshaven, Germany; ZIB, Zuse Institute Berlin, Berlin-Dahlem, Germany; Department of Geosciences, University of Bremen, Bremen, Germany; BAM, Bundesanstalt fur Materialforschung und -prufung, Berlin, Germany; Advanced Photon Source, Argonne National Laboratory, Argonne, USA; Feinberg School of Medicine, Northwestern University, Chicago, USA

During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). (…) Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. (…) Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources.

How Amira-Avizo Software is used

The cavity segmentation, performed on the bryozoan, the marble block and the dendrophyllid coral, consists of three steps: (i) threshold segmentation of the organism skeletons and marble with the Segmentation Editor (not performed on the ophiuroid tooth); (ii) running the Ambient Occlusion Field module on the background label (‘material’ within Amira) containing the air within the object and the object-surrounding space (…) As last step (iii), threshold segmentations of the cavity space were carried out within the Segmentation Editor on the AO field and AO-derived fields.